4UBD Viral Protein Immune System date Aug 12, 2014
title Crystal Structure Of A Neutralizing Human Monoclonal Antibod 1968 H3 Ha
authors D.A.Shore, H.Yang, M.Cho, R.O.Donis, J.Stevens
compound source
Molecule: Hemagglutinin Ha1 Chain
Chain: A, U, I, M, Q, E
Engineered: Yes
Organism_scientific: Influenza A Virus
Organism_taxid: 506350
Strain: Ahong Kong11968 H3n2
Gene: Ha
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Hemagglutinin Ha2 Chain
Chain: V, F, B, J, N, R
Engineered: Yes

Organism_scientific: Influenza A Virus
Organism_taxid: 506350
Strain: Ahong Kong11968 H3n2
Gene: Ha
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111

Molecule: Monoclonal Antibody H Chain
Chain: C, Y, G, S, O, K
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029

Molecule: Monoclonal Antibody L Chain
Chain: D, X, H, T, P, L
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
symmetry Space Group: P 31
R_factor 0.212 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
128.700 128.700 428.319 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.50 Å
ligand BMA, MAN, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E, Q, M, I, U


F, J, N, B, V, R


Primary referenceA potent broad-spectrum protective human monoclonal antibody crosslinking two haemagglutinin monomers of influenza A virus., Wu Y, Cho M, Shore D, Song M, Choi J, Jiang T, Deng YQ, Bourgeois M, Almli L, Yang H, Chen LM, Shi Y, Qi J, Li A, Yi KS, Chang M, Bae JS, Lee H, Shin J, Stevens J, Hong S, Qin CF, Gao GF, Chang SJ, Donis RO, Nat Commun. 2015 Jul 21;6:7708. doi: 10.1038/ncomms8708. PMID:26196962
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1859 Kb) [Save to disk]
  • Biological Unit Coordinates (4ubd.pdb1.gz) 1842 Kb
  • LPC: Ligand-Protein Contacts for 4UBD
  • CSU: Contacts of Structural Units for 4UBD
  • Structure Factors (1902 Kb)
  • Retrieve 4UBD in mmCIF format [Save to disk]
  • Re-refined 4ubd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4UBD in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4UBD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 4ubd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ubd_F] [4ubd_T] [4ubd_P] [4ubd_U] [4ubd] [4ubd_C] [4ubd_M] [4ubd_X] [4ubd_B] [4ubd_N] [4ubd_A] [4ubd_H] [4ubd_L] [4ubd_S] [4ubd_G] [4ubd_J] [4ubd_O] [4ubd_Q] [4ubd_Y] [4ubd_D] [4ubd_V] [4ubd_R] [4ubd_K] [4ubd_E] [4ubd_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4UBD: [IG_like] [IGv ] by SMART
  • Other resources with information on 4UBD
  • Community annotation for 4UBD at PDBWiki (http://pdbwiki.org)

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